ST_ML Class Reference

#include <st_ml.hxx>

Inheritance diagram for ST_ML:

Collaboration diagram for ST_ML:

Public Member Functions
	ST_ML (GBDATA *gb_main)
	~ST_ML ()
void	create_column_statistic (AW_root *awr, const char *awarname, AW_awar *awar_default_alignment)
ColumnStat *	get_column_statistic ()
GB_ERROR	calc_st_ml (const char *tree_name, const char *alignment_name, const char *species_names, int marked_only, ColumnStat *colstat, const WeightedFilter *weighted_filter) __ATTR__USERESULT
void	cleanup ()
const AP_filter *	get_filter () const
size_t	get_filtered_length () const
size_t	get_alignment_length () const
ST_rate_matrix &	get_matrix_for (int distance)
GBDATA *	get_gb_main () const
const TreeNode *	get_gbt_tree () const
size_t	count_species_in_tree () const
AP_tree *	find_node_by_name (const char *species_name)
void	set_postcalc_callback (WindowCallbackSimple postcalc_cb_, AW_window *cb_window_)
void	do_postcalc_callback ()
size_t	get_first_pos () const
size_t	get_last_pos () const
double	get_step_size () const
const ST_base_vector *	get_inv_base_frequencies () const
const ST_base_vector &	get_base_frequency_at (size_t pos) const
float	get_rate_at (size_t pos) const
void	set_modified (int *what=NULp)
void	set_refresh ()
void	clear_all ()
MostLikelySeq *	get_ml_vectors (const char *species_name, AP_tree *node, size_t start_ali_pos, size_t end_ali_pos)
ST_ML_Color *	get_color_string (const char *species_name, AP_tree *node, size_t start_ali_pos, size_t end_ali_pos)
bool	update_ml_likelihood (char *result[4], int &latest_update, const char *species_name, AP_tree *node)
int	refresh_needed ()

Detailed Description

Definition at line 111 of file st_ml.hxx.

Constructor & Destructor Documentation

ST_ML::ST_ML

(

GBDATA *

gb_main

)

Definition at line 314 of file ST_ml.cxx.

ST_ML::~ST_ML

(

)

Definition at line 339 of file ST_ml.cxx.

References GBS_free_hash().

Member Function Documentation

void ST_ML::create_column_statistic	(	AW_root *	awr,
		const char *	awarname,
		AW_awar *	awar_default_alignment
	)

Definition at line 867 of file ST_ml.cxx.

References get_gb_main().

Referenced by STAT_create_main_window().

ColumnStat* ST_ML::get_column_statistic ( )

inline

Definition at line 175 of file st_ml.hxx.

Referenced by st_ok_cb(), and STAT_create_main_window().

GB_ERROR ST_ML::calc_st_ml	(	const char *	tree_name,
		const char *	alignment_name,
		const char *	species_names,
		int	marked_only,
		ColumnStat *	colstat,
		const WeightedFilter *	weighted_filter
	)

Definition at line 491 of file ST_ml.cxx.

References ARB_strdup(), AWT_KEEP_MARKED, AWT_REMOVE_ZOMBIES, ColumnStat::calculate(), cleanup(), GB_transaction::close(), count_species_in_tree(), WeightedFilter::create_aliview(), error(), GB_await_error(), GB_MIND_CASE, GB_read_clock(), GBS_create_hash(), GBS_free_hash(), GBS_global_string(), GBS_hash_do_loop(), GBS_write_hash(), GBT_get_alignment_len(), GBT_get_species_count(), GBT_link_tree(), get_filtered_length(), ColumnStat::get_rates(), ColumnStat::get_ttratio(), AP_filter::is_invalid(), AP_tree_root::loadFromDB(), NULp, AP_tree_root::remove_leafs(), st_assert, arb_progress::subtitle(), ta, tree_size_ok(), and weights.

Referenced by st_ml_check_sequence_quality(), and st_ok_cb().

void ST_ML::cleanup

(

)

Definition at line 472 of file ST_ml.cxx.

References GBS_free_hash(), NULp, and MostLikelySeq::tmp_out.

Referenced by calc_st_ml().

const AP_filter * ST_ML::get_filter

(

)

const

Definition at line 887 of file ST_ml.cxx.

References ARB_seqtree_root::get_filter().

Referenced by get_alignment_length(), get_filtered_length(), and st_ml_check_sequence_quality().

size_t ST_ML::get_filtered_length

(

)

const

Definition at line 888 of file ST_ml.cxx.

References get_filter(), and AP_filter::get_filtered_length().

Referenced by calc_st_ml(), st_ml_check_sequence_quality(), and update_ml_likelihood().

size_t ST_ML::get_alignment_length

(

)

const

Definition at line 889 of file ST_ml.cxx.

References get_filter(), and AP_filter::get_length().

Referenced by get_color_string(), and update_ml_likelihood().

ST_rate_matrix& ST_ML::get_matrix_for ( int  distance )

inline

Definition at line 190 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), and MostLikelySeq::calculate_ancestor().

GBDATA* ST_ML::get_gb_main ( ) const

inline

Definition at line 194 of file st_ml.hxx.

Referenced by create_column_statistic(), st_ok_cb(), and STAT_create_main_window().

const TreeNode * ST_ML::get_gbt_tree

(

)

const

Definition at line 871 of file ST_ml.cxx.

Referenced by st_ml_check_sequence_quality().

size_t ST_ML::count_species_in_tree

(

)

const

Definition at line 875 of file ST_ml.cxx.

References info, and ARB_tree_info::leafs.

Referenced by calc_st_ml().

AP_tree * ST_ML::find_node_by_name

(

const char *

species_name

)

Definition at line 881 of file ST_ml.cxx.

References GBS_read_hash(), and NULp.

Referenced by STAT_find_node_by_name().

void ST_ML::set_postcalc_callback ( WindowCallbackSimple  postcalc_cb_, AW_window *  cb_window_  )

inline

Definition at line 200 of file st_ml.hxx.

Referenced by STAT_set_postcalc_callback().

void ST_ML::do_postcalc_callback ( )

inline

Definition at line 204 of file st_ml.hxx.

Referenced by st_ok_cb().

size_t ST_ML::get_first_pos ( ) const

inline

Definition at line 206 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), MostLikelySeq::calculate_ancestor(), and MostLikelySeq::set_sequence().

size_t ST_ML::get_last_pos ( ) const

inline

Definition at line 207 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), MostLikelySeq::calculate_ancestor(), and MostLikelySeq::set_sequence().

double ST_ML::get_step_size ( ) const

inline

Definition at line 209 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), and MostLikelySeq::calculate_ancestor().

const ST_base_vector* ST_ML::get_inv_base_frequencies ( ) const

inline

Definition at line 211 of file st_ml.hxx.

Referenced by MostLikelySeq::set_sequence().

const ST_base_vector& ST_ML::get_base_frequency_at ( size_t  pos ) const

inline

Definition at line 212 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out().

float ST_ML::get_rate_at ( size_t  pos ) const

inline

Definition at line 213 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), and MostLikelySeq::calculate_ancestor().

void ST_ML::set_modified

(

int *

what = NULp

)

void ST_ML::set_refresh

(

)

void ST_ML::clear_all

(

)

Definition at line 662 of file ST_ml.cxx.

References GB_read_clock(), and ta.

Referenced by MostLikelySeq::sequence_change().

MostLikelySeq * ST_ML::get_ml_vectors	(	const char *	species_name,
		AP_tree *	node,
		size_t	start_ali_pos,
		size_t	end_ali_pos
	)

Definition at line 679 of file ST_ml.cxx.

References MostLikelySeq::calc_out(), TreeNode::father, MostLikelySeq::forget_sequence(), GBS_read_hash(), TreeNode::get_brother(), TreeNode::leftlen, NULp, TreeNode::rightlen, seq, TreeNode::set_root(), st_assert, and ST_MAX_SEQ_PART.

Referenced by get_color_string(), st_ml_add_sequence_part_to_stat(), and update_ml_likelihood().

ST_ML_Color * ST_ML::get_color_string	(	const char *	species_name,
		AP_tree *	node,
		size_t	start_ali_pos,
		size_t	end_ali_pos
	)

(Re-)Calculates the color string of a given node for sequence positions [start_ali_pos .. end_ali_pos[

Definition at line 794 of file ST_ml.cxx.

References ARB_calloc(), ST_base_vector::b, DNA_Table::char_to_enum(), MostLikelySeq::color_out, MostLikelySeq::color_out_valid_till, GB_read_char_pntr(), GBS_read_hash(), get_alignment_length(), MostLikelySeq::get_bound_species_data(), get_ml_vectors(), GET_ML_VECTORS_BUG_WORKAROUND_INCREMENT, LD_BUCKET_SIZE, max, ST_base_vector::max_frequency(), min, NULp, ST_BUCKET_SIZE, ST_UNKNOWN, start, and MostLikelySeq::tmp_out.

Referenced by STAT_get_color_string().

bool ST_ML::update_ml_likelihood	(	char *	result[4],
		int &	latest_update,
		const char *	species_name,
		AP_tree *	node
	)

calculates values for 'Detailed column statistics' in ARB_EDIT4

Returns

true if calculated with sucess

Parameters

result	if result[0] is NULp, memory will be allocated and assigned to result[0 .. 3]. You should NOT allocate result yourself, but you can reuse it for multiple calls.
latest_update	has to contain and will be set to the latest statistic modification time (0 is a good start value)
species_name	name of the species (for which the column statistic shall be calculated)
node	of the current tree (for which the column statistic shall be calculated)

Note: either 'species_name' or 'node' needs to be specified, but NOT BOTH

Definition at line 725 of file ST_ml.cxx.

References ARB_calloc(), ST_base_vector::b, DNA_Table::char_to_enum(), GBS_read_hash(), get_alignment_length(), get_filtered_length(), get_ml_vectors(), GET_ML_VECTORS_BUG_WORKAROUND_INCREMENT, min, NULp, st_assert, ST_base_vector::summarize(), and MostLikelySeq::tmp_out.

Referenced by STAT_update_ml_likelihood().

int ST_ML::refresh_needed

(

)

---

The documentation for this class was generated from the following files:

• STAT/st_ml.hxx
• STAT/ST_ml.cxx